mfarlow: Anyone know why that is happening?
It's happening because you let them die. :p
...okay, now the serious answer. In the vanilla game, when an NPC dies while in your party — whether from friendly fire or otherwise — a glitch reduces their reaction to you down to 0 (or lower). IIRC, this should've been fixed by the UAP (Drog Blacktooth's Unofficial Arcanum Patch). Go to the stickied thread at the top of this board, and download and install the patch; then start a new game so all the bugfixes will be in effect.
Otherwise your best bet, as DeMignon suggested, is to reload an earlier game if you have one.
And a protip: Don't just rely on the quicksave and quick load keys; create your own restore points along the way by fully saving the game with a unique name at least once a session, or whenever a milestone of some sort has been reached.